Antelop

A user-friendly software package for systems neuroscience data management

Rory Bedford

MRC LMB

Big data in neuroscience

  • New technologies such as Neuropixels allow us to record an increasingly high number of units
  • Continual shift towards more automated behavioural assays means longer/more recordings
  • Scientists have to spend more time on data processing workflows and data management
  • Increasingly advanced skills are needed to undertake this (HPC skills, data engineering, etc.)

Data engineering challenges

  • Custom file formats/project structures are hard to parse
  • Custom preprocessing/analysis scripts are very difficult to reproduce
  • Lab data storage not centralised
  • High entry barrier to existing tools like DataJoint and NWB which makes their adoption difficult for many labs

Our solution: Antelop

  • Software package designed to facilitate the easy adoption of data processing and storage best practices
  • Simple pip install and straightforward graphical configuration
  • Extensive graphical user interface for all aspects of your data management and processing
  • MySQL database backend for centralised storage
  • Supports electrophysiology, calcium imaging, and behavioural data processing with HPC integration

Our solution: Antelop

  • Integrates with existing tools, such as popular spikesorters, CaImAn, and DeepLabCut
    • Leverages the fact that preprocessing requirements for common acquisition methods are fairly uniform
  • Implements a range of data visualisation tools and metrics out of the box, including an analysis standard library
  • Supports the writing of custom analysis scripts, with direct integration to your lab’s GitHub and data immutability checks for reproducibility
  • Has import/export functions for NWB and a range of acquisition systems
  • Has an opinionated but accomodating database structure to facilitate large-scale modelling

Publishing

  • Working on a preprint at present
  • We aim to publish by May this year
  • Python package has been released but is undergoing extensive testing
  • Documentation available

Thank you